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Overview of Targetfinder.org PDF Print
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Thursday, 19 March 2009 22:27

Introduction

The prediction of specific transcription factor target genes is a major challenge in systems biology and functional genomics. Current sequence-based methods yield many false predictions, due to the short and degenerated DNA-binding motifs. We provide a tool for a new systematic genome-wide approach using the seed-distribution-distance method, that searches large-scale genome-wide expression data for genes that are similarly expressed as known targets. This method allows to identify genes that are likely targets, allowing sequence-based methods to focus on a subset of genes, giving rise to fewer false-positive predictions. ...

What do you need to provide

  • list of known target genes

What do you get

  • ranked list of genes with names and links to and
  • detailed information about the mapping of your data to the internal database
  • cross-validation with a recovery test (graphical output and raw data)
  • List of potential new targets filtered according to binding affinity of given transcription factors   

How does it work?

The overall idea of targetfinder.org is that genes that share a transcription factor binding site in their promoter are co-regulated. If a user of targetfinder.org provides a list of genes which he knows are regulated by a certain transcription factor, targetfinder.org searches for genes that show a similarly expression pattern in a large microarray pannel of more than 1200 experiments. A second property, the binding affinity is used to give a combined prediction of potential new targets.

 

 

 

Last Updated on Friday, 05 February 2010 22:26
 
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